TT_BDMI Class Reference

#include <ttbdmi.h>

Inheritance diagram for TT_BDMI:

Collaboration diagram for TT_BDMI:

Public Member Functions
	TT_BDMI ()
	TT_BDMI (const TT_BDMI &T)
virtual	~TT_BDMI ()
void	set_sequence (bitstring **seq)
void	inherit_haplo (TTrait *mother, TTrait *father)
void	inherit_diplo (TTrait *mother, TTrait *father)
void	mutate_haplo ()
void	mutate_diplo ()
double	viability_haplo ()
double	viability_diplo ()
unsigned int	get_num_mut_haplo (unsigned int loc)
unsigned int	get_num_mut_diplo (unsigned int loc)
Setters:
void	set_nb_locus (int val)
void	set_mut_rate (double val)
void	set_geno_rate (double val)
void	set_recomb_rate (double val)
void	set_isHaploid (bool val)
void	set_inherit_func_ptr (void(TT_BDMI::*theFunc)(TTrait *, TTrait *))
void	set_mutation_func_ptr (void(TT_BDMI::*theFunc)(void))
void	set_viability_func_ptr (double(TT_BDMI::*theFunc)(void))
void	set_proto (TProtoBDMI *proto)
Implementations
virtual void	init ()
virtual void	init_sequence ()
virtual void	reset ()
virtual void	inherit (TTrait *mother, TTrait *father)
virtual void	mutate ()
virtual void *	set_trait (void *value)
virtual void	set_sequence (void **seq)
virtual void	set_value ()
virtual void *	getValue () const
virtual trait_t	get_type () const
virtual void **	get_sequence () const
virtual double	get_allele_value (int loc, int all)
virtual void	set_allele_value (unsigned int locus, unsigned int allele, double value)
virtual void	show_up ()
virtual TT_BDMI *	clone ()
virtual TT_BDMI &	operator= (const TTrait &)
virtual bool	operator== (const TTrait &)
virtual bool	operator!= (const TTrait &)
virtual void	store_data (BinaryStorageBuffer *saver)
virtual bool	retrieve_data (BinaryStorageBuffer *reader)
Public Member Functions inherited from TTrait
virtual void	init ()=0
	Called to allocate the trait's genotypic sequences. More...
virtual void	init_sequence ()=0
	Called at the start of each replicate, sets the initial genotypes. More...
virtual void	reset ()=0
	Called at the end of each simulation/replicate, deallocates sequence memory. More...
virtual void	inherit (TTrait *mother, TTrait *father)=0
	Inheritance procedure, creates a new trait from mother's and father's traits. More...
virtual void	mutate ()=0
	Mutation procedure, perform mutations on the genes sequence. More...
virtual void *	set_trait (void *value)=0
	Called to set the phenotypic to a particular value or to give context-dependant value(s) to the trait. More...
virtual void	set_sequence (void **seq)=0
	Called to set the sequence pointer to an existing trait. More...
virtual double	get_allele_value (int loc, int all)=0
	Called to read one allele value at a particular locus. More...
virtual void	set_allele_value (unsigned int locus, unsigned int allele, double value)=0
	Called to change the allelic value at a particular locus. More...
virtual void	set_value ()=0
	Tells the trait to set its phenotype from genotype, should be used instead of getValue(). More...
virtual void *	getValue () const =0
	Genotype to phenotype mapper. More...
virtual trait_t	get_type () const =0
	type accessor. More...
virtual void **	get_sequence () const =0
	sequence accessor. More...
virtual void	show_up ()=0
	Writes some info to stdout. More...
virtual TTrait *	clone ()=0
	Returns a copy of itself. More...
virtual	~TTrait ()
Public Member Functions inherited from StorableComponent
virtual void	store_data (BinaryStorageBuffer *saver)=0
	Interface to store the component data (e.g. gene values) into a binary buffer. More...
virtual bool	retrieve_data (BinaryStorageBuffer *reader)=0
	Interface to retrieve the same data from the binary buffer. More...
virtual	~StorableComponent ()

Private Attributes
TProtoBDMI *	_myProto
bitstring *	_sequence [2]
double	_phenotype
bool	_isHaploid
unsigned int	_nb_locus
double	_mut_rate
double	_genomic_mut_rate
double	_recomb_rate
void(TT_BDMI::*	_inherit_func_ptr )(TTrait *, TTrait *)
void(TT_BDMI::*	_mutation_func_ptr )(void)
double(TT_BDMI::*	_viability_func_ptr )(void)

Static Private Attributes
static unsigned int *	_recomb_template
static unsigned int *	_rSites
static unsigned char *	_sites
static unsigned int	_haploGenotCoding [2][2] = {{0,1},{2,3}}
static unsigned int	_diploGenotCoding [2][2] = {{0,1},{1,2}}

Constructor & Destructor Documentation

TT_BDMI() [1/2]

TT_BDMI::TT_BDMI ( )

inline

  : _myProto(0), _phenotype(0), _isHaploid(0), _nb_locus(0), _mut_rate(0), _genomic_mut_rate(0),
  _recomb_rate(0), _inherit_func_ptr(0), _mutation_func_ptr(0), _viability_func_ptr(0)
  {_sequence[0] = _sequence[1] = NULL;}

References _sequence.

Referenced by clone().

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TT_BDMI() [2/2]

TT_BDMI::TT_BDMI ( const TT_BDMI &  T )

inline

  : _myProto(T._myProto), _phenotype(0), _isHaploid(T._isHaploid), _nb_locus(T._nb_locus),
  _mut_rate(T._mut_rate), _genomic_mut_rate(T._genomic_mut_rate), _recomb_rate(T._recomb_rate), 
  _inherit_func_ptr(T._inherit_func_ptr), _mutation_func_ptr(T._mutation_func_ptr),
  _viability_func_ptr(T._viability_func_ptr)
  {_sequence[0] = _sequence[1] = NULL;}

References _sequence.

~TT_BDMI()

virtual TT_BDMI::~TT_BDMI ( )

inlinevirtual

{ }

Member Function Documentation

clone()

virtual TT_BDMI * TT_BDMI::clone ( )

inlinevirtual

Implements TTrait.

{return new TT_BDMI(*this);}

References TT_BDMI().

get_allele_value()

double TT_BDMI::get_allele_value ( int  loc, int  all  )

virtual

Implements TTrait.

{
  if(_isHaploid)
          return _myProto->getGenoFitnessHaplo(loc, all);
  else
          return _myProto->getGenoFitnessDiplo(loc, all);
}

References _isHaploid, _myProto, TProtoBDMI::getGenoFitnessDiplo(), and TProtoBDMI::getGenoFitnessHaplo().

get_num_mut_diplo()

unsigned int TT_BDMI::get_num_mut_diplo ( unsigned int  loc )

inline

{return (*_sequence[0])[loc]+(*_sequence[1])[loc];}

References _sequence.

Referenced by TTBDMI_SH::countAllele_diplo().

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get_num_mut_haplo()

unsigned int TT_BDMI::get_num_mut_haplo ( unsigned int  loc )

inline

{return (*_sequence[0])[loc];}

References _sequence.

Referenced by TTBDMI_SH::countAllele_haplo().

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get_sequence()

virtual void ** TT_BDMI::get_sequence ( ) const

inlinevirtual

Implements TTrait.

{return (void**)&_sequence[0];}

References _sequence.

get_type()

virtual trait_t TT_BDMI::get_type ( ) const

inlinevirtual

Implements TTrait.

{return _myProto->get_type();}

References _myProto, and TProtoBDMI::get_type().

getValue()

virtual void * TT_BDMI::getValue ( ) const

inlinevirtual

Implements TTrait.

{return (void*)&_phenotype;}

References _phenotype.

Referenced by show_up().

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inherit()

virtual void TT_BDMI::inherit ( TTrait *  mother, TTrait *  father  )

inlinevirtual

Implements TTrait.

{(this->* _inherit_func_ptr) (mother, father);}

References _inherit_func_ptr.

inherit_diplo()

void TT_BDMI::inherit_diplo	(	TTrait *	mother,
		TTrait *	father
	)

{
  bitstring** mother_seq = (bitstring**)mother->get_sequence();
  bitstring** father_seq = (bitstring**)father->get_sequence();
  
  _myProto->inherit(FEM, _sequence[FEM], mother_seq);
  _myProto->inherit(MAL, _sequence[MAL], father_seq);
}

References _myProto, _sequence, FEM, TTrait::get_sequence(), TProtoBDMI::inherit(), and MAL.

Referenced by TProtoBDMI::setParameters().

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inherit_haplo()

void TT_BDMI::inherit_haplo	(	TTrait *	mother,
		TTrait *	father
	)

{
  bitstring* gamete[2];
  gamete[0] = (bitstring*)(mother->get_sequence()[0]);
  gamete[1] = (bitstring*)(father->get_sequence()[0]);
  
  _myProto->inherit(MAL, _sequence[0], &gamete[0]);
}

References _myProto, _sequence, TTrait::get_sequence(), TProtoBDMI::inherit(), and MAL.

Referenced by TProtoBDMI::setParameters().

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init()

void TT_BDMI::init ( )

virtual

Implements TTrait.

{  
  if(_sequence[0] != NULL) fatal("TT_BDMI::init::_sequence[0] is not NULL !\n"); 
  if(!_isHaploid && _sequence[1] != NULL) fatal("TT_BDMI::init::_sequence[1] is not NULL !\n");
  
  _sequence[0] = new bitstring(_nb_locus);
  if(!_isHaploid) _sequence[1] = new bitstring(_nb_locus);
}

References _isHaploid, _nb_locus, _sequence, and fatal().

Referenced by operator=(), and set_sequence().

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init_sequence()

void TT_BDMI::init_sequence ( )

virtual

Implements TTrait.

{
  if(_sequence[0] == NULL) _sequence[0] = new bitstring(_nb_locus);
  
  _sequence[0]->reset();  //sets all bits to 0
  
  if(!_isHaploid){
    if(_sequence[1] == NULL) _sequence[1] = new bitstring(_nb_locus);
    _sequence[1]->reset();
  }
 
  if(_myProto->isInitSet()) {
 
    for(unsigned int i = 0; i < _nb_locus; i++) {
      if( RAND::Uniform() < _myProto->get_init_freq(i) ) 
        _sequence[0]->set(i);
      
      if( !_isHaploid )
        if ( RAND::Uniform() < _myProto->get_init_freq(i) )
          _sequence[1]->set(i);
    } 
  }
 
}

References _isHaploid, _myProto, _nb_locus, _sequence, TProtoBDMI::get_init_freq(), TProtoBDMI::isInitSet(), bitstring::reset(), bitstring::set(), and RAND::Uniform().

Referenced by LCE_Init_BDMI::init_value().

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mutate()

virtual void TT_BDMI::mutate ( )

inlinevirtual

Implements TTrait.

{(this->*_mutation_func_ptr)();}

References _mutation_func_ptr.

mutate_diplo()

void TT_BDMI::mutate_diplo

(

)

{
  unsigned int NbMut;
  
  NbMut = (unsigned int)RAND::Poisson(_genomic_mut_rate);
  
  while(NbMut != 0) {  
    
    _sequence[ RAND::RandBool() ]->flip(  RAND::Uniform( _nb_locus ) );
    
    NbMut--;
  }
}

References _genomic_mut_rate, _nb_locus, _sequence, bitstring::flip(), RAND::Poisson(), RAND::RandBool(), and RAND::Uniform().

Referenced by TProtoBDMI::setParameters().

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mutate_haplo()

void TT_BDMI::mutate_haplo

(

)

{
  unsigned int NbMut;
  
  NbMut = (unsigned int)RAND::Poisson(_genomic_mut_rate);
  
  while(NbMut != 0) {  
    
    _sequence[0]->flip(  RAND::Uniform( _nb_locus ) );
    
    NbMut--;
  }
}

References _genomic_mut_rate, _nb_locus, _sequence, bitstring::flip(), RAND::Poisson(), and RAND::Uniform().

Referenced by TProtoBDMI::setParameters().

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operator!=()

bool TT_BDMI::operator!= ( const TTrait &  T )

virtual

Implements TTrait.

{
  if(!((*this) == T))
    return true;
  else
    return false;
}

operator=()

TT_BDMI & TT_BDMI::operator= ( const TTrait &  T )

virtual

Implements TTrait.

{
  const TT_BDMI& TD = dynamic_cast<const TT_BDMI&> (T);
  if(this != &TD) {
    
    _nb_locus = TD._nb_locus;
//    _mut_rate = TD._mut_rate;
//    _recomb_rate = TD._recomb_rate;
//    _genomic_mut_rate = TD._genomic_mut_rate;
    _isHaploid = TD._isHaploid;
//    _inherit_func_ptr = TD._inherit_func_ptr;
//    _mutation_func_ptr = TD._mutation_func_ptr;
//    _viability_func_ptr = TD._viability_func_ptr;
    //deallocate any previous _sequence memory:
    reset();
    //allocate _sequence memory:
    init();
    //copy _sequence:
    _sequence[0]->copy(*TD._sequence[0]);
    if(!_isHaploid) _sequence[1]->copy(*TD._sequence[1]);
    
    set_value();
  }
  return *this;
}

References _isHaploid, _nb_locus, _sequence, bitstring::copy(), init(), reset(), and set_value().

operator==()

bool TT_BDMI::operator== ( const TTrait &  T )

virtual

Implements TTrait.

{
  if(_myProto->get_type().compare(T.get_type()) != 0) return false;
  
  const TT_BDMI& TD = dynamic_cast<const TT_BDMI&> (T);
  if(this != &TD) {
    if(_nb_locus != TD._nb_locus) return false;
    if(_isHaploid != TD._isHaploid) return false;
  }
  return true;
}

References _isHaploid, _myProto, _nb_locus, TProtoBDMI::get_type(), and TTrait::get_type().

reset()

void TT_BDMI::reset ( )

virtual

Implements TTrait.

{
  if(_sequence[0] != NULL) delete _sequence[0];
  if(!_isHaploid && _sequence[1] != NULL) delete _sequence[1];
  
  _sequence[0] = NULL;
  _sequence[1] = NULL;
}

References _isHaploid, and _sequence.

Referenced by operator=(), and set_sequence().

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retrieve_data()

bool TT_BDMI::retrieve_data ( BinaryStorageBuffer *  reader )

virtual

Implements StorableComponent.

{
  size_t wnb = _sequence[0]->nb_words();
  size_t bytes = wnb * sizeof(bitstring::_ul);
  bitstring::_ul *srce = new bitstring::_ul [wnb];
 
  reader->read(srce, bytes);
  _sequence[0]->set_data(srce,wnb);
 
  if(!_isHaploid){
    reader->read(srce, bytes);
    _sequence[1]->set_data(srce,wnb);
  }
 
  delete [] srce;
 
  return true;
}

References _isHaploid, _sequence, bitstring::nb_words(), BinaryStorageBuffer::read(), and bitstring::set_data().

set_allele_value()

void TT_BDMI::set_allele_value ( unsigned int  locus, unsigned int  allele, double  value  )

virtual

Implements TTrait.

{
  _myProto->setGenoFitnessValue(locus, allele, value);
}

References _myProto, and TProtoBDMI::setGenoFitnessValue().

set_geno_rate()

void TT_BDMI::set_geno_rate ( double  val )

inline

{_genomic_mut_rate = val;}

References _genomic_mut_rate.

Referenced by TProtoBDMI::hatch().

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set_inherit_func_ptr()

void TT_BDMI::set_inherit_func_ptr ( void(TT_BDMI::*)(TTrait *, TTrait *)  theFunc )

inline

                                                                        {_inherit_func_ptr = theFunc;}

References _inherit_func_ptr.

Referenced by TProtoBDMI::hatch().

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set_isHaploid()

void TT_BDMI::set_isHaploid ( bool  val )

inline

{_isHaploid = val;}

References _isHaploid.

Referenced by TProtoBDMI::hatch().

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set_mut_rate()

void TT_BDMI::set_mut_rate ( double  val )

inline

{_mut_rate = val;}

References _mut_rate.

Referenced by TProtoBDMI::hatch().

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set_mutation_func_ptr()

void TT_BDMI::set_mutation_func_ptr ( void(TT_BDMI::*)(void)  theFunc )

inline

                                                                        {_mutation_func_ptr = theFunc;}

References _mutation_func_ptr.

Referenced by TProtoBDMI::hatch().

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set_nb_locus()

void TT_BDMI::set_nb_locus ( int  val )

inline

{_nb_locus = val;}

References _nb_locus.

Referenced by TProtoBDMI::hatch().

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set_proto()

void TT_BDMI::set_proto ( TProtoBDMI *  proto )

inline

{_myProto = proto;}

References _myProto.

Referenced by TProtoBDMI::hatch().

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set_recomb_rate()

void TT_BDMI::set_recomb_rate ( double  val )

inline

{_recomb_rate = val;}

References _recomb_rate.

set_sequence() [1/2]

void TT_BDMI::set_sequence

(

bitstring **

seq

)

{
  reset(); init();
  _sequence[0]->copy(*seq[0]);
  if(!_isHaploid) _sequence[1]->copy(*seq[1]);
}

References _isHaploid, _sequence, bitstring::copy(), init(), and reset().

set_sequence() [2/2]

virtual void TT_BDMI::set_sequence ( void **  seq )

inlinevirtual

Implements TTrait.

{}

set_trait()

virtual void * TT_BDMI::set_trait ( void *  value )

inlinevirtual

Implements TTrait.

{return NULL;}

set_value()

virtual void TT_BDMI::set_value ( )

inlinevirtual

Implements TTrait.

{_phenotype = (this->*_viability_func_ptr)();}

References _phenotype, and _viability_func_ptr.

Referenced by LCE_Init_BDMI::init_value(), operator=(), and show_up().

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set_viability_func_ptr()

void TT_BDMI::set_viability_func_ptr ( double(TT_BDMI::*)(void)  theFunc )

inline

                                                                        {_viability_func_ptr = theFunc;}

References _viability_func_ptr.

Referenced by TProtoBDMI::hatch().

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show_up()

void TT_BDMI::show_up ( )

virtual

Implements TTrait.

{
  set_value();
  std::cout<<"\n   Trait type: dmi"
  <<"\n        value: "<<*(double*)getValue()
  <<"\n     num loci: "<<_nb_locus
  <<"\nfitness table: "<<endl;
  _myProto->showGenoTable(_nb_locus/2);
  
  cout<<"\n     sequence: "<<endl;
  cout<<"0: ";
  for(unsigned int i = 0; i < _nb_locus && i < 64; i++)
    cout<<(unsigned int)(*_sequence[0])[i];
  cout<<endl;
  
  if(!_isHaploid) {
    cout<<"1: ";
    for(unsigned int i = 0; i < _nb_locus && i < 64; i++)
      cout<<(unsigned int)(*_sequence[1])[i];
  }
  cout<<endl;
}

References _isHaploid, _myProto, _nb_locus, _sequence, getValue(), set_value(), and TProtoBDMI::showGenoTable().

store_data()

void TT_BDMI::store_data ( BinaryStorageBuffer *  saver )

virtual

Implements StorableComponent.

{
  size_t wnb = _sequence[0]->nb_words();
  size_t bytes = sizeof(bitstring::_ul);
 
  for(size_t i = 0; i < wnb; i++)
    saver->store(_sequence[0]->getword_atIdx(i), bytes);
 
  if(!_isHaploid){
    for(size_t i = 0; i < wnb; i++)
      saver->store(_sequence[1]->getword_atIdx(i), bytes);
  }
}

References _isHaploid, _sequence, bitstring::getword_atIdx(), bitstring::nb_words(), and BinaryStorageBuffer::store().

viability_diplo()

double TT_BDMI::viability_diplo

(

)

{
  unsigned int npair = _nb_locus/2;
  double viab = 1;
//cout << "\nTT_BDMI::viability_diplo\n";
//  cout << "  sequence[0].size(): "<<(*_sequence[0]).size()
//  << "  sequence[0].nb_words(): "<<(*_sequence[0]).nb_words()<<endl;
//  cout << "  sequence[1].size(): "<<(*_sequence[1]).size()
//  << "  sequence[1].nb_words(): "<<(*_sequence[1]).nb_words()<<endl;
  
  for (unsigned int pair = 0, i = 0; pair < npair && i < _nb_locus; ++pair) {
    viab *= 1 + _myProto->getGenoFitnessDiplo( pair , //locus number
            _diploGenotCoding[ (*_sequence[0])[i] ][ (*_sequence[1])[i] ], //first locus
            _diploGenotCoding[ (*_sequence[0])[i+1] ][ (*_sequence[1])[i+1] ]); //second locus
    i += 2;
  }
  return viab; 
}

References _diploGenotCoding, _myProto, _nb_locus, _sequence, and TProtoBDMI::getGenoFitnessDiplo().

Referenced by TProtoBDMI::setParameters().

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viability_haplo()

double TT_BDMI::viability_haplo

(

)

{
  unsigned int npair = _nb_locus/2;
  double viab = 1;
  
  for (unsigned int pair = 0, i = 0; pair < npair && i < _nb_locus; ++pair) {
    viab *= 1 + _myProto->getGenoFitnessHaplo( pair , 
                          _haploGenotCoding[ (*_sequence[0])[i] ][ (*_sequence[0])[i+1] ]);
    i += 2;
  }
  return viab;
}

References _haploGenotCoding, _myProto, _nb_locus, _sequence, and TProtoBDMI::getGenoFitnessHaplo().

Referenced by TProtoBDMI::setParameters().

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Member Data Documentation

_diploGenotCoding

unsigned int TT_BDMI::_diploGenotCoding = {{0,1},{1,2}}

staticprivate

Referenced by viability_diplo().

_genomic_mut_rate

double TT_BDMI::_genomic_mut_rate

private

Referenced by mutate_diplo(), mutate_haplo(), and set_geno_rate().

_haploGenotCoding

unsigned int TT_BDMI::_haploGenotCoding = {{0,1},{2,3}}

staticprivate

Referenced by viability_haplo().

_inherit_func_ptr

void(TT_BDMI::* TT_BDMI::_inherit_func_ptr) (TTrait *, TTrait *)

private

Referenced by inherit(), and set_inherit_func_ptr().

_isHaploid

bool TT_BDMI::_isHaploid

private

Referenced by get_allele_value(), init(), init_sequence(), operator=(), operator==(), reset(), retrieve_data(), set_isHaploid(), set_sequence(), show_up(), and store_data().

_mut_rate

double TT_BDMI::_mut_rate

private

Referenced by set_mut_rate().

_mutation_func_ptr

void(TT_BDMI::* TT_BDMI::_mutation_func_ptr) (void)

private

Referenced by mutate(), and set_mutation_func_ptr().

_myProto

TProtoBDMI* TT_BDMI::_myProto

private

Referenced by get_allele_value(), get_type(), inherit_diplo(), inherit_haplo(), init_sequence(), operator==(), set_allele_value(), set_proto(), show_up(), viability_diplo(), and viability_haplo().

_nb_locus

unsigned int TT_BDMI::_nb_locus

private

Referenced by init(), init_sequence(), mutate_diplo(), mutate_haplo(), operator=(), operator==(), set_nb_locus(), show_up(), viability_diplo(), and viability_haplo().

_phenotype

double TT_BDMI::_phenotype

private

Referenced by getValue(), and set_value().

_recomb_rate

double TT_BDMI::_recomb_rate

private

Referenced by set_recomb_rate().

_recomb_template

unsigned int* TT_BDMI::_recomb_template

staticprivate

_rSites

unsigned int * TT_BDMI::_rSites

staticprivate

_sequence

bitstring* TT_BDMI::_sequence[2]

private

Referenced by get_num_mut_diplo(), get_num_mut_haplo(), get_sequence(), inherit_diplo(), inherit_haplo(), init(), init_sequence(), mutate_diplo(), mutate_haplo(), operator=(), reset(), retrieve_data(), set_sequence(), show_up(), store_data(), TT_BDMI(), viability_diplo(), and viability_haplo().

_sites

unsigned char* TT_BDMI::_sites

staticprivate

_viability_func_ptr

double(TT_BDMI::* TT_BDMI::_viability_func_ptr) (void)

private

Referenced by set_value(), and set_viability_func_ptr().

---

The documentation for this class was generated from the following files:

• ttbdmi.h
• ttbdmi.cc